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Table 2 Hybrid assemblies of bacterial strains with simulated Illumina short reads and low-quality Oxford Nanopore long reads using MaSuRCA, SPAdes, and Unicycler

From: Benchmarking hybrid assembly approaches for genomic analyses of bacterial pathogens using Illumina and Oxford Nanopore sequencing

Strain Number of contigs Total length (bp) GC content (%)
MaSuRCA SPAdes Unicycler MaSuRCA SPAdes Unicycler MaSuRCA SPAdes Unicycler
Pseudomonas aeruginosa PAO1 4 (0 cir.; 8 dead) 64 1 (0 cir.; 2 dead) 6,173,430 6,261,368 6,264,384 66.55 66.57 66.56
Escherichia coli O157:H7 Sakai 6 (0 cir.; 12 dead) 550 83 (0 cir.; 6 dead) 5,503,884 5,487,649 5,562,446 50.50 50.38 50.45
Bacillus anthracis Ames Ancestor 7 (0 cir.; 14 dead) 78 3 (0 cir.; 6 dead) 5,433,227 5,482,457 5,489,222 35.26 35.17 35.23
Klebsiella variicola DSM 15968 1 (0 cir.; 2 dead) 121 1 (0 cir.; 2 dead) 5,482,918 5,505,259 5,520,752 57.54 57.57 57.56
Salmonella Typhimurium LT2 3 (0 cir.; 6 dead) 78 3 (0 cir.; 3 dead) 4,848,561 4,952,963 4,947,288 52.22 52.24 52.24
Cronobacter sakazakii ATCC 29544 18 (0 cir.; 36 dead) 72 4 (1 cir.; 6 dead) 4,492,402 4,640,822 4,663,144 56.60 56.67 56.64
Clostridium botulinum CDC_1632 2 (1 cir.; 2 dead) 109 11 (0 cir.; 2 dead) 4,398,971 4,379,115 4,372,396 28.04 27.95 27.92
Listeria monocytogenes EGD-e 4 (1 cir.; 6 dead) 11 1 (0 cir.; 2 dead) 2,927,219 2,933,282 2,942,862 38.02 37.94 37.97
Staphylococcus aureus NCTC 8325 3 (0 cir.; 6 dead) 37 1 (0 cir.; 2 dead) 2,759,087 2,818,488 2,821,119 32.88 32.84 32.87
Campylobacter jejuni NCTC 11168 1 (0 cir.; 2 dead) 8 1 (0 cir.; 2 dead) 1,630,638 1,640,924 1,641,330 30.56 30.55 30.55
  1. acir., circularized contigs
  2. bdead, dead ends